1887

Abstract

A rod-shaped marine bacterium, designated CL-Z59, was isolated from seawater enriched with zooplankton. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CL-Z59 belongs to the genus , the highest level of sequence similarity (99.2 %) being found with respect to KCCM 42681. However, DNA–DNA hybridization experiments between strain CL-Z59 and KCCM 42681 revealed a mean relatedness value of 33 %. Cells were Gram-positive, strictly aerobic and non-motile. Strain CL-Z59 grew optimally at pH 6–7 and 25–30 °C and at a NaCl concentration of 3 %. The isolate was characterized chemotaxonomically as having -diaminopimelic acid in the cell wall. The major isoprenoid quinone was MK-8(H) and the predominant cellular fatty acid was iso-C. The DNA G+C content was 73.3 mol%. On the basis of phylogenetic, genotypic and phenotypic data, strain CL-Z59 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CL-Z59 (=KCCM 42320=DSM 18239).

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2008-09-01
2022-01-20
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References

  1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J.(1990). Basic local alignment search tool. J Mol Biol 215, 403–410.[CrossRef] [Google Scholar]
  2. An, D.-S., Im, W.-T., Lee, S.-T. & Yoon, M.-H.(2007).Nocardioides panacihumi sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 57, 2143–2146.[CrossRef] [Google Scholar]
  3. Cho, J. C. & Giovannoni, S. J.(2004). Cultivation and growth characteristics of a diverse group of oligotrophic marine Gammaproteobacteria. Appl Environ Microbiol 70, 432–440.[CrossRef] [Google Scholar]
  4. Choi, D. H., Kim, H. M., Noh, J.-H. & Cho, B. C.(2007).Nocardioides marinus sp. nov. Int J Syst Evol Microbiol 57, 775–779.[CrossRef] [Google Scholar]
  5. Cole, J. R., Chai, B., Marsh, T. L., Farris, R. J., Wang, Q., Kulam, S. A., Chandra, S., McGarrell, D. M., Schmidt, T. M. & other authors(2003). The Ribosomal Database Project (RDP-ll): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31, 442–443.[CrossRef] [Google Scholar]
  6. Collins, M. D.(1985). Analysis of isoprenoid quinones. Methods Microbiol 18, 329–366. [Google Scholar]
  7. Collins, M. D., Dorsch, M. & Stackebrandt, E.(1989). Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov. Int J Syst Bacteriol 39, 1–6.[CrossRef] [Google Scholar]
  8. Collins, M. D., Cockcroft, S. & Wallbanks, S.(1994). Phylogenetic analysis of a new ll-diaminopimelic acid-containing coryneform bacterium from herbage, Nocardioides plantarum sp. nov. Int J Syst Bacteriol 44, 523–526.[CrossRef] [Google Scholar]
  9. Englen, M. D. & Kelley, L. C.(2000). A rapid DNA isolation procedure for the identification of Campylobacter jejuni by the polymerase chain reaction. Lett Appl Microbiol 31, 421–426.[CrossRef] [Google Scholar]
  10. Fitch, W. M.(1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.[CrossRef] [Google Scholar]
  11. Hansen, G. H. & Sørheim, R.(1991). Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 13, 231–241.[CrossRef] [Google Scholar]
  12. Holt, J. G., Krieg, N. R., Sneath, P. H. A., Staley, J. T. & Williams, S. T.(1994). Nocardioform actinomycetes. In ShorterBergey's Manual of Determinative Bacteriology, pp. 625–650. Edited by W. R. Hensyl. Baltimore: Williams & Wilkins.
  13. Jensen, H. L.(1934). Studies on saprophytic mycobacteria and corynebacteria. Proc Linn Soc N S W 59, 19–61. [Google Scholar]
  14. Jeon, Y.-S., Chung, H., Park, S., Hur, I., Lee, J.-H. & Chun, J.(2005). jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 21, 3171–3173.[CrossRef] [Google Scholar]
  15. Jukes, T. H. & Cantor, C. R.(1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  16. Kim, Y.-G., Choi, D. H., Hyun, S. & Cho, B. C.(2007).Oceanobacillus profundus sp. nov., isolated from a deep-sea sediment core. Int J Syst Evol Microbiol 57, 409–413.[CrossRef] [Google Scholar]
  17. Kubota, M., Kawahara, K., Sekiya, K., Uchida, T., Hattori, Y., Futamata, H. & Hiraishi, A.(2005).Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments. Syst Appl Microbiol 28, 165–174.[CrossRef] [Google Scholar]
  18. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  19. Lane, D. J.(1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
  20. Lawson, P. A., Collins, M. D., Schumann, P., Tindall, B. J., Hirsch, P. & Labrenz, M.(2000). New ll-diaminopimelic acid-containing actinomycetes from hypersaline, heliothermal and meromictic Antarctic Ekho Lake: Nocardioides aquaticus sp. nov. and Friedmanniella lacustris sp. nov. Syst Appl Microbiol 23, 219–229.[CrossRef] [Google Scholar]
  21. Lee, S. D.(2007).Nocardioides furvisabuli sp. nov., isolated from black sand. Int J Syst Evol Microbiol 57, 35–39.[CrossRef] [Google Scholar]
  22. Lee, D. W., Hyun, C.-G. & Lee, S. D.(2007).Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand. Int J Syst Evol Microbiol 57, 2960–2963.[CrossRef] [Google Scholar]
  23. Lee, S. D., Lee, D. W. & Kim, J.-S.(2008).Nocardioides hwasunensis sp. nov. Int J Syst Evol Microbiol 58, 278–281.[CrossRef] [Google Scholar]
  24. Lemos, M. L., Toranzo, A. E. & Barja, J. L.(1985). Modified medium for the oxidation-fermentation test in the identification of marine bacteria. Appl Environ Microbiol 49, 1541–1543. [Google Scholar]
  25. Lyman, J. & Fleming, R. H.(1940). Composition of sea water. J Mar Res 3, 134–146. [Google Scholar]
  26. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. & Parlett, J. H.(1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef] [Google Scholar]
  27. Prauser, H.(1976).Nocardioides, a new genus of the order Actinomycetales. Int J Syst Bacteriol 26, 58–65.[CrossRef] [Google Scholar]
  28. Prauser, H.(1984).Nocardioides luteus spec. nov. Z Allg Mikrobiol 24, 647–648.[CrossRef] [Google Scholar]
  29. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  30. Schippers, A., Schumann, P. & Spröer, C.(2005).Nocardioides oleivorans sp. nov., a novel crude-oil-degrading bacterium. Int J Syst Evol Microbiol 55, 1501–1504.[CrossRef] [Google Scholar]
  31. Smibert, R. M. & Krieg, N. R.(1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  32. Stackebrandt, E. & Goebel, B. M.(1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.[CrossRef] [Google Scholar]
  33. Staneck, J. L. & Roberts, G. D.(1974). Simplified approach to the identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28, 226–231. [Google Scholar]
  34. Suzuki, K. & Komagata, K.(1983).Pimelobacter gen. nov., a new genus of coryneform bacteria with ll-diaminopimelic acid in the cell wall. J Gen Appl Microbiol 29, 59–71.[CrossRef] [Google Scholar]
  35. Tamaoka, J. & Komagata, K.(1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.[CrossRef] [Google Scholar]
  36. Tóth, E. M., Kéki, Z., Homonnay, Z. G., Borsodi, A. K., Márialigeti, K. & Schumann, P.(2008).Nocardioides daphniae sp. nov., isolated from Daphnia cucullata (Crustacea: Cladocera). Int J Syst Evol Microbiol 58, 78–83.[CrossRef] [Google Scholar]
  37. Yi, H. & Chun, J.(2004a).Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54, 2151–2154.[CrossRef] [Google Scholar]
  38. Yi, H. & Chun, J.(2004b).Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54, 1295–1299.[CrossRef] [Google Scholar]
  39. Yoon, J.-H., Rhee, S.-K., Lee, J.-S., Park, Y.-H. & Lee, S.-T.(1997).Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column. Int J Syst Bacteriol 47, 933–938.[CrossRef] [Google Scholar]
  40. Yoon, J.-H., Cho, Y.-G., Lee, S. T., Suzuki, K.-I., Nakase, T. & Park, Y.-H.(1999).Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium. Int J Syst Bacteriol 49, 675–680.[CrossRef] [Google Scholar]
  41. Yoon, J.-H., Kim, I.-G., Kang, K. H., Oh, T.-K. & Park, Y.-H.(2004).Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea. Int J Syst Evol Microbiol 54, 71–75.[CrossRef] [Google Scholar]
  42. Yoon, J.-H., Kim, I.-G., Lee, M.-H., Lee, C.-H. & Oh, T.-K.(2005a).Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea. Int J Syst Evol Microbiol 55, 809–814.[CrossRef] [Google Scholar]
  43. Yoon, J.-H., Kim, I.-G., Lee, M.-H. & Oh, T.-K.(2005b).Nocardioides kribbensis sp. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 55, 1611–1614.[CrossRef] [Google Scholar]
  44. Yoon, J.-H., Lee, C.-H. & Oh, T.-K.(2005c).Nocardioides dubius sp. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 55, 2209–2212.[CrossRef] [Google Scholar]
  45. Yoon, J.-H., Lee, C.-H. & Oh, T.-K.(2006a).Nocardioides lentus sp. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 56, 271–275.[CrossRef] [Google Scholar]
  46. Yoon, J.-H., Lee, J.-K., Jung, S.-Y., Kim, J.-A., Kim, H.-K. & Oh, T.-K.(2006b).Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium. Int J Syst Evol Microbiol 56, 1783–1787.[CrossRef] [Google Scholar]
  47. Yoon, J.-H., Kang, S.-J., Lee, C.-H. & Oh, T.-K.(2007a).Nocardioides insulae sp. nov., isolated from soil. Int J Syst Evol Microbiol 57, 136–140.[CrossRef] [Google Scholar]
  48. Yoon, J.-H., Kang, S.-J., Lee, S.-Y. & Oh, T.-K.(2007b).Nocardioides terrigena sp. nov., isolated from soil. Int J Syst Evol Microbiol 57, 2472–2475.[CrossRef] [Google Scholar]
  49. Yoon, J.-H., Kang, S.-J., Lee, M.-H. & Oh, T.-K.(2008).Nocardioides hankookensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 58, 434–437.[CrossRef] [Google Scholar]
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